Such expressions as that famous one of Linnæus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications (Darwin, 1859, p. 413f).

Friday, 1 May 2009

Paraphyly Watch 2: Paraphyly & the Catalogue of Life

A recent draft discussion document, Towards a management hierarchy (classification) for the Catalogue of Life (Gordon, 2009), contains a discussion on paraphyly:"It is not the purpose here to summarise the various viewpoints but a need to consider what we want from a classification is inescapable. Cavalier-Smith (1998) has given a useful discussion. One bone of contention in recent decades has been whether or not to allow the use of paraphyletic taxa in classification. A paraphyletic taxon is a monophyletic group that does not contain all the descendents (derivatives) of that group. One of the best-known examples is that of Reptilia, nominally a class of Chordata. Since it is agreed that birds (nominally class Aves) have a reptilian ancestor, and Reptilia by convention does not include Aves, then Reptilia is a paraphyletic group. But paraphyletic groups potentially abound at all levels of the taxonomic hierarchy. Indeed, there are many thousands of taxa where it is not yet known if they are paraphyletic (including some of the descendants) or holophyletic (including all of the descendants). Cavalier-Smith's classical understanding of monophyly is pragmatic, including both paraphyletic and holophyletic groups. On this understanding, Reptilia + Aves [+ Mammalia] is holophyletic whereas Reptilia alone is merely paraphyletic; either way, both are monophyletic" (Gordon, 2009, Online). Note the definition of paraphyly: "A paraphyletic taxon is a monophyletic group that does not contain all the descendents (derivatives) of that group". This is of course an incorrect definition of paraphyly. Moreover, it uses monophyly to validate paraphyly as a 'natural' group. Paraphyly is an artificial assemblage of unrelated taxa. Dubious definitions of paraphyly fall under the category of misuse, thus making Gordon (2009) a contender for the coveted Pewter Leprechaun. But Gordon (2009) goes further: "Since it is agreed that birds (nominally class Aves) have a reptilian ancestor …" Is it? If reptiles are a group of unrelated taxa, that is some 'reptiles' are more closely related to mammals than they are to other reptiles, then it would mean birds would have multiple ancestors and therefore multiple origins. Gordon (2009) does not stop there: "Cavalier-Smith’s classical understanding of monophyly is pragmatic, including both paraphyletic and holophyletic groups. On this understanding, Reptilia + Aves [+ Mammalia] is holophyletic whereas Reptilia alone is merely paraphyletic; either way, both are monophyletic." This is a case of abuse. Reptila cannot be automatically assumed to be monophyletic just because grouping them with mammals and birds results in a monophyletic group.

The draft manuscript is a typical protest for paraphyletic groups commonly made by evolutionary taxonomists in places like Taxon or Taxacom. The usual comments are made such as plea for 'traditional Darwinian classification' and confusing cladistics with phylogenetic classification. I do hope that the problem of paraphyly is not over-looked in the final manuscript. Who am I kidding? Of course it will!

1 comment:

David Marjanović
said...

Interestingly, and contrary to pronouncements by Mayr and many others, the definition of "monophyletic" as a synonym of the younger "holophyletic" is older than the one as a cover term for "paraphyletic" + "holophyletic". I might be able to find a reference for this in about 20 hours.